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I believe a guided tour with exclusive guide is if you want to do the tour with a guide with only people you already know. You join a group if you don't mind going along with people you don't already know. (Both groups being under 15 people)

We did a tour of the museums early in the morning on a different day. We weren't going to use a tour company except that they get in so early. We planned to ditch the tour once we got inside. The tour was actually good so we stayed with them. The tour lasted 5 hours despite the advertized 3 hour time:

We did it on different days and were glad we did because the museum tour was tiring. It may be pushing it, but you should be able to do the museum tour before the Scavi tour.

Here's an excerpt from my trip report:

Got up early to go meet our Vatican Museum tour. The only tour we took. We got there at 7:45 and met our guide by the bus stop outside the Vatican Museums. Lines were already pretty long but our guide had positioned the rest of our tour group close to the front of the line. We didn’t have a very long wait to go in. We used Argiletum Tours which had been recommended by our hostess. They were cheap at 44e including admission. We had only 9 people in the tour and we had the headsets so we could hear our guide. He was very knowledgeable with good English. He had us head straight to the Cistine Chapel. There were maybe 20 other people in there with us. When we went back later, there were hundreds in there, shoulder to shoulder. The museums are amazing. We left the tour which continued into the Basilica at noon because we were exhausted and had already been in the Basilica.

Haven't done the night tour, but lighting might be a factor if you want to take photos.